Hepatitis B virus (HBV) with a stop mutation at precore codon 28 (TGG to TAG, tryptophan to stop) was investigated in the serum of hepatocellular carcinoma patients with hepatitis B surface antigen (73 from Korea; 14 of Japanese ancestry in Hawaii). Among these, hepatitis B virus DNA was detectable in 64 (88%) patients from Korea and 9 (64%) patients from Hawaii, using polymerase chain reaction. Among patients with direct sequencing results, this mutation was identified in 50/58 (86%) patients from Korea and 9/9 (100%) of those from Hawaii. Among patients with this mutant HBV, 21/50 (42%) patients from Korea and 1/9 (11%) from Hawaii were coinfected as well with wild-type HBV. The prevalence of the mutant virus (without co-infection with wild-type HBV) among patients with hepatitis B e antigen (23/28[82%]) was not different from that in patients without it (27/30 [90%]). Generally, it was expected that patients with hepatitis B e antigen would be infected with wild-type HBV and those without hepatitis B e antigen were expected to have the mutant HBV. However, 10/28 (36%) patients with hepatitis B e antigen had the mutant HBV alone. These data suggest that HBV with the precore codon 28 stop mutation may contribute to the development of hepatocellular carcinoma and this mutation often is not correlated with the absence of hepatitis B e antigen. During a 16-month period in 1991-1992, blood samples and questionnaire data were obtained from 65 incident cases of hepatocellular carcinoma (HCC) as well as from 2 control groups of hospitalized patients matched on gender and age, which included 65 metastatic liver cancer patients and 65 patients hospitalized for eye, ear, nose or throat conditions. The odds ratio (with 95% confidence intervals) in logistic regression modeling comparing the HCC cases to the combined control series were 18.8 (8.2-43.2) for the presence of hepatitis B surface antigen and 7.7 (1.7- 35.1) for antibody to the hepatitis C virus (anti-HCV).